[English] 日本語
Yorodumi
- PDB-1ykq: Crystal structure of Diels-Alder ribozyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ykq
TitleCrystal structure of Diels-Alder ribozyme
Components(Diels-Alder ribozyme) x 2
KeywordsRNA / carbon-carbon bond / catalytic mechanism / RNA crystal structure / Diels-Alder reaction / ribozyme
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSerganov, A. / Keiper, S. / Malinina, L. / Tereshko, V. / Skripkin, E. / Hobartner, C. / Polonskaia, A. / Phan, A.T. / Wombacher, R. / Micura, R. ...Serganov, A. / Keiper, S. / Malinina, L. / Tereshko, V. / Skripkin, E. / Hobartner, C. / Polonskaia, A. / Phan, A.T. / Wombacher, R. / Micura, R. / Dauter, Z. / Jaschke, A. / Patel, D.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation.
Authors: Serganov, A. / Keiper, S. / Malinina, L. / Tereshko, V. / Skripkin, E. / Hobartner, C. / Polonskaia, A. / Phan, A.T. / Wombacher, R. / Micura, R. / Dauter, Z. / Jaschke, A. / Patel, D.J.
History
DepositionJan 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diels-Alder ribozyme
B: Diels-Alder ribozyme
C: Diels-Alder ribozyme
D: Diels-Alder ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,25116
Polymers31,5194
Non-polymers73212
Water00
1
A: Diels-Alder ribozyme
B: Diels-Alder ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1708
Polymers15,7592
Non-polymers4106
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Diels-Alder ribozyme
D: Diels-Alder ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0828
Polymers15,7592
Non-polymers3226
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.690, 44.240, 79.640
Angle α, β, γ (deg.)90.00, 107.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: C / End label comp-ID: C / Refine code: 6

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA101 - 1111 - 11
21CC101 - 1111 - 11
12BB201 - 2381 - 38
22DD201 - 2381 - 38

NCS ensembles :
ID
1
2

-
Components

#1: RNA chain Diels-Alder ribozyme


Mass: 3497.146 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence was derived from the in vitro selected ribozyme catalyzing Diels-Alder reaction between tethered anthracene and biotinylated maleimide
#2: RNA chain Diels-Alder ribozyme


Mass: 12262.333 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence was derived from the in vitro selected ribozyme catalyzing Diels-Alder reaction between tethered anthracene and biotinylated maleimide
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.04 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG400, sodium cacodylate, magnesium acetate, 1,6-hexandiol, sodium chloride, cadmium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG40011
2sodium cacodylate11
3H2O11
4PEG40012
5sodium cacodylate12
6magnesium acetate12
71,6-hexandiol12
8sodium chloride12
9cadmium chloride12
10H2O12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2004
RadiationMonochromator: Si(111),(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. all: 6902 / Num. obs: 6744 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 8.1
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.8 / Num. unique all: 673 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Diels-Alder ribozyme from the ribozyme-product complex, pdb entry 1YLS

1yls


Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.852 / SU B: 109.285 / SU ML: 0.73 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.671 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3238 312 4.8 %random
Rwork0.2857 ---
obs0.2875 6563 97.6 %-
all-6564 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å20 Å21.26 Å2
2---8.91 Å20 Å2
3---7.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.755 Å
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2078 12 0 2090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212320
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.61233610
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021018
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2620.21209
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it033325
X-RAY DIFFRACTIONr_scangle_it04.53610
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A230loose positional0.485
2B809loose positional0.385
1A230loose thermal010
2B809loose thermal010
LS refinement shellResolution: 3.5→3.588 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 24
Rwork0.364 447
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9947-0.0839-1.10693.8868-0.13124.1616-0.20320.3208-0.0009-0.16770.50060.51160.4317-0.0485-0.2973-0.1432-0.10550.0076-0.03350.0686-0.21434.890326.316523.0536
22.32-0.62452.56012.5376-0.87964.4194-0.25390.2170.3499-0.40120.3263-0.4412-0.5310.2039-0.0724-0.0431-0.08490.02270.0349-0.1458-0.163858.188733.343822.9837
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A101 - 111
2X-RAY DIFFRACTION1B201 - 238
3X-RAY DIFFRACTION1A249
4X-RAY DIFFRACTION1B240 - 246
5X-RAY DIFFRACTION2C101 - 111
6X-RAY DIFFRACTION2D201 - 238
7X-RAY DIFFRACTION2D340 - 348
8X-RAY DIFFRACTION2C349

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more